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Yorodumi- PDB-2vm5: HUMAN BIR2 DOMAIN OF BACULOVIRAL INHIBITOR OF APOPTOSIS REPEAT- C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vm5 | ||||||
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Title | HUMAN BIR2 DOMAIN OF BACULOVIRAL INHIBITOR OF APOPTOSIS REPEAT- CONTAINING 1 (BIRC1) | ||||||
Components | BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 1 | ||||||
Keywords | APOPTOSIS | ||||||
Function / homology | Function and homology information IPAF inflammasome complex / icosanoid biosynthetic process / canonical inflammasome complex / protein serine/threonine kinase binding / pattern recognition receptor signaling pathway / cysteine-type endopeptidase inhibitor activity / pyroptotic inflammatory response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / detection of bacterium ...IPAF inflammasome complex / icosanoid biosynthetic process / canonical inflammasome complex / protein serine/threonine kinase binding / pattern recognition receptor signaling pathway / cysteine-type endopeptidase inhibitor activity / pyroptotic inflammatory response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / detection of bacterium / positive regulation of interleukin-1 beta production / positive regulation of JNK cascade / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of inflammatory response / nervous system development / basolateral plasma membrane / regulation of apoptotic process / negative regulation of neuron apoptotic process / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / negative regulation of apoptotic process / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Herman, M.D. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Herman, M.D. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Structures of Bir Domains from Human Naip and Ciap2. Authors: Herman, M.D. / Moche, M. / Flodin, S. / Welin, M. / Tresaugues, L. / Johansson, I. / Nilsson, M.E. / Nordlund, P. / Nyman, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vm5.cif.gz | 36.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vm5.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/2vm5 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/2vm5 | HTTPS FTP |
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-Related structure data
Related structure data | 2uvlSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12376.056 Da / Num. of mol.: 1 / Fragment: BIR2 DOMAIN, RESIDUES 141-244 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) R3 PRARE / References: UniProt: Q13075 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 32.2 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 0.1M CITRIC ACID, PH 5, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97627 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97627 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 8726 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.02 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.93 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.13 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.86 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UVL Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.595 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 151-153 ARE DISORDERED. SER139 AND MET140 ARE FROM VECTOR SHOULD BE ASP AND ILE IN REAL SEQUENCE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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